Package: methVisual

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch methVisual_1.5.0.tar.gz

StartedAt: 2011-05-09 15:44:27 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 15:46:46 -0700 (Mon, 09 May 2011)

EllapsedTime: 139.1 seconds

RetCode: 0

Status:  OK

CheckDir: methVisual.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/methVisual.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methVisual/DESCRIPTION’ ... OK
* this is package ‘methVisual’ version ‘1.5.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘methVisual’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘methVisual.pdf’ from 295Kb to 138Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘methVisual’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: IRanges

Attaching package: ‘IRanges’

The following object(s) are masked from ‘package:base’:

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: proto
Loading required package: DBI
Loading required package: RSQLite
Loading required package: RSQLite.extfuns
Loading required package: chron
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘methVisual.Rnw’ 
** testing if installed package can be loaded

* DONE (methVisual)

name	user	system	elapsed
Cooccurrence	0.905	0.033	0.954
MethAlignNW	2.550	0.059	2.756
MethDataInput	0.063	0.017	0.090
MethLollipops	0.016	0.001	0.019
MethylQC	2.178	0.046	2.450
cgInAlign	0.003	0.001	0.005
cgMethFinder	0.001	0.000	0.001
coversionGenom	0	0	0
findNonAligned	0.004	0.002	0.006
heatMapMeth	0.124	0.003	0.127
makeDataMethGFF	0.575	0.060	0.664
makeLocalExpDir	0.054	0.018	0.140
makeTabFilePath	0.017	0.001	0.019
matrixSNP	0.434	0.016	0.455
methCA	0.021	0.004	0.025
methData	0.002	0.001	0.004
methFisherTest	0.055	0.003	0.058
methWhitneyUTest	0.006	0.001	0.007
plotAbsMethyl	0.004	0.001	0.005
plotMatrixSNP	0.946	0.025	1.067
readBisulfFASTA	0.061	0.021	0.122
selectRefSeq	0.057	0.019	0.098